I've never read Faction War, but the 5e treatment of Planescape certainly seems to imply that it's after FW to me. The fact that some factions have disappeared or been replaced by others, and some have faded into minor faction status, etc, and that all the old 2e ones are acknowledged as having been major factions in the recent past seems to set the 5e version after the 2e material. But again, having not read FW, I could be missing some crucial bits of information that would make me read it the other way.